Variant report

Variant	rs9353321
Chromosome Location	chr6:86260756-86260757
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:121483913..121485978-chr6:86260101..86262043,2	MCF-7	breast:
2	chr6:86258544..86261104-chr6:86387142..86389153,2	K562	blood:
3	chr6:86258616..86262862-chr6:86386972..86389770,3	K562	blood:
4	chr6:86260582..86262333-chr6:86283688..86285782,2	K562	blood:

Variant related genes	Relation type
ENSG00000203875	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs12528808	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12664908	0.84[ASN][1000 genomes]
rs2229524	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3812137	0.93[ASN][1000 genomes]
rs3812139	0.93[ASN][1000 genomes]
rs4144166	0.81[ASN][1000 genomes]
rs4327657	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4373339	0.81[ASN][1000 genomes]
rs4400191	0.81[ASN][1000 genomes]
rs4565270	0.81[ASN][1000 genomes]
rs59744370	0.85[EUR][1000 genomes]
rs6900270	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6902638	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6902904	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6910543	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913634	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6923017	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6930543	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6930790	1.00[ASN][1000 genomes]
rs6942065	0.81[ASN][1000 genomes]
rs73751215	0.93[ASN][1000 genomes]
rs7744309	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745560	0.80[AFR][1000 genomes]
rs7746186	0.81[ASN][1000 genomes]
rs7749600	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7752105	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7753022	0.84[ASN][1000 genomes]
rs7771187	0.93[ASN][1000 genomes]
rs7771366	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7775788	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9344527	0.81[ASN][1000 genomes]
rs9344528	0.81[ASN][1000 genomes]
rs9344529	0.81[ASN][1000 genomes]
rs9344530	0.93[ASN][1000 genomes]
rs9344538	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9351063	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9351066	0.85[EUR][1000 genomes]
rs9353319	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9353323	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9353324	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9359655	0.81[ASN][1000 genomes]
rs9359656	0.87[ASN][1000 genomes]
rs9362223	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9362224	0.87[ASN][1000 genomes]
rs9362225	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9362226	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9444353	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9444356	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9450280	0.81[ASN][1000 genomes]
rs9450286	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9450289	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450294	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450295	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450299	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9450300	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450304	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450307	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450308	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450309	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450313	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	esv3326486	chr6:86020165-86292456	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv3435075	chr6:86052235-86271910	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv463937	chr6:86114766-86264374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv604092	chr6:86114766-86264374	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv886333	chr6:86199243-86289415	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv463939	chr6:86205323-86279737	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv470839	chr6:86205323-86279737	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv604093	chr6:86205323-86279737	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv886334	chr6:86214507-86394403	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
12	esv1792638	chr6:86224053-86336300	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
13	nsv516516	chr6:86234835-86278691	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9353321	NT5E	cis	Thyroid	GTEx
rs9353321	NT5E	cis	Whole Blood	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86208800-86284600	Weak transcription	Small Intestine	intestine
2	chr6:86208800-86289200	Weak transcription	Pancreas	Pancrea
3	chr6:86218400-86266200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:86221800-86285800	Weak transcription	Fetal Brain Male	brain
5	chr6:86222600-86289400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:86223400-86262800	Weak transcription	Stomach Mucosa	stomach
7	chr6:86223400-86285000	Weak transcription	Brain Substantia Nigra	brain
8	chr6:86223800-86262600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr6:86224000-86279000	Weak transcription	NHLF	lung
10	chr6:86224200-86302600	Weak transcription	Colonic Mucosa	Colon
11	chr6:86230000-86263000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:86231200-86285000	Weak transcription	Hela-S3	cervix
13	chr6:86233400-86262200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr6:86233600-86262400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:86233800-86289200	Weak transcription	Spleen	Spleen
16	chr6:86234000-86261000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:86236600-86279000	Weak transcription	HMEC	breast
18	chr6:86241400-86283600	Weak transcription	Fetal Kidney	kidney
19	chr6:86243200-86285200	Weak transcription	Psoas Muscle	Psoas
20	chr6:86243200-86286000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr6:86243400-86269600	Weak transcription	Brain Anterior Caudate	brain
22	chr6:86243400-86301400	Weak transcription	Thymus	Thymus
23	chr6:86243600-86285000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr6:86243600-86285800	Weak transcription	Fetal Brain Female	brain
25	chr6:86243600-86286200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:86243800-86284800	Weak transcription	Brain Angular Gyrus	brain
27	chr6:86244000-86262800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr6:86244000-86265400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr6:86244200-86279000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr6:86244200-86286000	Weak transcription	Right Ventricle	heart
31	chr6:86244200-86289200	Weak transcription	Gastric	stomach
32	chr6:86244400-86281000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr6:86245800-86261000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr6:86246400-86279000	Weak transcription	NHEK	skin
35	chr6:86246600-86265000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr6:86246600-86270800	Weak transcription	HUVEC	blood vessel
37	chr6:86246600-86274200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr6:86247800-86262600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:86248200-86271200	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr6:86248600-86261200	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr6:86250200-86284800	Weak transcription	Aorta	Aorta
42	chr6:86252800-86261000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:86252800-86284400	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr6:86252800-86289600	Weak transcription	Esophagus	oesophagus
45	chr6:86253000-86261000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr6:86253400-86261000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr6:86253400-86261000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr6:86253400-86286000	Weak transcription	Brain Germinal Matrix	brain
49	chr6:86254800-86271400	Weak transcription	Colon Smooth Muscle	Colon
50	chr6:86254800-86287800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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